Investigating The Ways Domesticated Plants Change in Past and Future Climates

Using innovative techniques to understand environmental responses of major agricultural crops

About 12,000 years ago, hunters and gatherers around the world began to cultivate plants, leading to the domestication of our major cereals, legumes, and tuberous crops. This was one of the premiere developments in human history, because without agricultural economies based on domesticated plants everything considered integral to our current way of life—including the development of food surpluses, craft specialization, state level societies, and institutions—would not be possible. Dr. Dolores Piperno, Senior Scientist and Curator of South American Archaeology Emerita at the Smithsonian Institution in Washington D.C. and Panama, investigates how major crops such as maize, squashes, and beans were domesticated by past human populations, while studying the plants’ responses to past, current, and future environments. Her innovative research reveals the ways these plants once adapted and will adapt (or not) to future environments in terms of their overall growth, genetics, seed yield, and nutritional quality. These findings will be crucial to geneticists, botanists, and breeders who seek to understand how crops will respond to predicted higher atmospheric CO2 and temperature, and decreased rainfall in the future.

Plant domestication was an evolutionary process. The earliest farmers performed gene breeding (though they didn’t know it at the time) as they selected for beneficial attributes, such as larger and nontoxic seeds, fruits, and tubers. In the process, they bred out other traits important to the crops’ wild progenitors for adapting the plants to the natural environment. Maize’s wild progenitor, called teosinte, thus contains more genetic diversity than maize and conserving these and other progenitors including by maintaining wild seed banks also becomes of utmost importance. Plants like maize may still have some ability to adjust to drought and temperature changes and ward off pests, but these as well as teosinte’s responses must be studied through experimental work. Dr. Piperno’s research involves studying plant responses of this kind, which include those known as phenotypic or developmental plasticity, a newly re-emerged and important element of plant adaptation. Developmental plasticity is the ability of plants to directly respond phenotypically (traits visible to the naked eye) to environmental changes, often through their gene expression changes (when DNA is copied into messenger RNA, called transcription), not through alterations in  DNA sequences. Dr. Piperno’s studies show how plant domestication occurred in the past, while providing critical information as to how plants will respond phenotypically and genetically to future environments.

Dr. Piperno’s multidisciplinary team at the Smithsonian comprises a plant physiologist, Klaus Winter, and a biologist, Irene Holst. Together they closely collaborate with three geneticists; Jeffrey Ross-Ibarra and Paul Gepts at University of California, Davis and Matthew Hufford of Iowa State University. Their work is among the first research that will document how important crops that feed the world today and their wild progenitors respond and adapt to past, present, and future environments. They expect to reach important milestones within two to three years. Their findings will provide important information to breeders and other scientists, as the possible range of future plant responses to climate change may significantly involve phenotypic plasticity and gene expression. 

Current and future research includes:

  • Using Novel Techniques to Study Phenotypic and Gene Expression Changes in Plants - The past environment in which plant domestication occurred was very different than today’s, as in many regions of the world atmospheric CO2, temperature, and rainfall were much lower. Dr. Piperno and her team grow teosinte and maize in two large glass environmental chambers at the Smithsonian Tropical Research Institute in Panama. The air’s CO2 and temperature are adjusted to those under which the plants were initially collected, cultivated, and domesticated 12,000 to 10,000 years ago. To do this, air is funneled through sofnolime, which removes the carbon and lowers the CO2. Similarly, temperature is lowered using large air conditioners. In one of the chambers CO2 and temperature is adjusted to modern conditions as the experimental control. As the plants grow and mature, phenotypic descriptions and gene expression studies are undertaken in order to explore and understand how different environmental conditions through time have influenced plant form and genetic responses. Gene expression work is carried out through sophisticated new methods that involve deep-sequencing technology (RNA-seq). Thus far, their experiment has produced a number of remarkable phenotypic and gene expression responses with significant differences from modern examples, including the development of important domestication traits previously thought to have been selected by human cultivators (e.g. in vegetative architecture, inflorescence sexuality, and seed maturation).
  • Undertaking Multigeneral Teosinte Cultivation in Past Conditions of CO2 and Temperature - Teosinte grown in Piperno’s research in past conditions that simulate those at the origins of maize domestication surprisingly resembles maize in its phenotypic traits considerably more than it does today, and gene expression responses also differ from those in modern environments. Modern teosinte currently forms the phenotypic and genetic baselines to study the maize domestication process; however, it appears that the last foragers and first cultivators worked with plants that were considerably different. Dr. Piperno works with these plants grown in past conditions. Her team will undertake multi-generational plant breeding in the conditions of CO2 and temperature known through paleoecological research to have prevailed at the origins of maize, by replanting year-by-year seeds from plants grown and selecting for important domestication traits known to have been chosen by early farmers. By replicating this selective breeding, their results will inform the phenotypic and underlying genetic processes that drove maize domestication and contribute to understanding how plant breeding may ameliorate teosinte and maize responses to future climate change.
  • Comparative Analysis of Gene Expression and Phenotypes in Past, Modern, and Future Conditions - Due to the continuous changes in climate, scientists project food security may become threatened by the year 2050. Dr. Piperno and her team are currently carrying out their first grow-out of maize and its wild progenitor in modeled future conditions of higher CO2 and temperature, using the projected values for 2050 (see brochure). Although crops have been and will continue to be cultivated under constantly changing environmental conditions, very little work has focused on the effects of these changes on crop phenotypes and genetics, including seed yield and nutritional quality. Piperno’s team will identify and measure these and other changes such as in plant height and biomass, and will study associated gene expression responses. Currently, Dr. Piperno and her team are growing maize and teosinte for this project. Experiments with beans and squashes will be incorporated within the next few years. The results of these studies will provide important information to scientists seeking to predict and ameliorate through genetic engineering and hybridization the future effects of environmental change on our important crop plants;for example, through the identification of genes and proteins related to drought, heat, and pest/pathogen stress.


Dr. Dolores Piperno has always been interested in human relationships with the plant world. During her graduate work at Temple University, she developed an interest in human adaptations to tropical forests, including the origins and dispersals of agriculture. During this time, the tropical forest was a widely understudied area. Some prominent scholars believed it had contributed little to New World cultural florescence, as it was thought to be too rainy, the vegetation too dense, and the soil too infertile for cultures to succeed. However, she first learned while studying early archaeological sites in Panama that people have thrived in those areas for a very long time, prominently by exploiting the plant world in numerous, sophisticated ways. The earliest New World agriculture, including with maize and squashes, is now known to be from the tropical forest. 

She and her research team have developed novel techniques to document plant exploitation and domestication in humid tropical climates for the first time. They found that people began to farm in the American tropical forest at the same time as the then better-studied regions such as southwest Asia and China, which had dominated the literature on agricultural origins and dispersals. Also interested in human relationships with the environment, Dr. Piperno looks at how natural environmental changes through time impact agricultural developments and vice versa. She has reconstructed ancient environments through micro-botanical studies of lake sediments, which have revealed archives of environmental change and human alterations of tropical landscapes from 20,000 years ago in Panama, Mexico, and elsewhere. 

Dr. Piperno is Senior Scientist and Curator of South American Archaeology Emerita at the Smithsonian Institution in Washington D.C. and Panama. She is fascinated with and motivated by the complexity of plant domestication; when one question is answered, many more emerge.


Election as Fellow of the American Association for the Advancement of Science

Election to the National Academy of Sciences

Election to the American Academy of Arts and Sciences

Orden de Vasco Nunez Award

Highest award given by Panama to a civilian. Awarded to Dr. Piperno for her contributions to understanding the prehistory of Panama

Pomerance Career Award from the Archaeological Institute of America